2  Getting started

We need access to required packages and obviously to the data with will further work with. I like to load all packages right at beginning of the document for a convenient overview of all required dependencies. I will point out some of the packages when we need them later.

# Data source
library(folio)

# Maps
library(rnaturalearth)

# Data wrangling, functional programming functions
library(dplyr)
library(purrr)

# Visualization
library(gt)
library(ggplot2)
library(showtext)
library(see) # half-violin plots
library(ggiraph)
library(htmltools)

# plot-table assembly
library(magick)
library(webshot2)
library(ggplotify)
library(patchwork)

# Table export
library(openxlsx2)

After loading the data, some preprocessing will be handy to avoid troubles and repetitive handling of the issues again and again. For example, in ?sec-advanced-design we will draw in earth map data to visualize countries. It turnes out that the {rnaturalearth} packages which is a common source of geographical data refers to Democratic Republic of the Congo, while the authors of the original publication use older name Zaire. Besides making this fix, we will also introduce an abbreviated version of the current country’s name to save some space in plot titles (also relevant in ?sec-advanced-design). We will also introduce C<sub>3</sub> and C<sub>4</sub> in the type column to set us for a nicely formatted spelling throughout all tables.

raw_dat_vegetation <- folio::vegetation

# Zaire was renamed in 1997
dat_vegetation <- raw_dat_vegetation |>
  mutate(
    country_label = case_when(
      country == "Zaire" ~ "Dem. Rep. of Congo",
      TRUE ~ country
    ),
    country = case_when(
      country == "Zaire" ~ "Democratic Republic of the Congo",
      TRUE ~ country
    )
  ) |> 
  # html for subscript in C3, C4
  mutate(type = case_when(
    type == "C3" ~ "C<sub>3</sub>",
    type == "C4" ~ "C<sub>4</sub>",
    TRUE ~ type
  ))

In some of the tables, we will refer to the data source in the table’s footnote and we thus create a reusable footnote label early on. Note markdown syntax for bold and monospace text:

# Data source footnote
folio_footnote <- "**Data source:** `vegetation` data from the `{folio}` package"